pynwb.spec module

class pynwb.spec.NWBRefSpec(target_type, reftype)

Bases: hdmf.spec.spec.RefSpec

Parameters:

• target_type (str) – the target type GroupSpec or DatasetSpec
• reftype (str) – the type of references this is i.e. region or object

class pynwb.spec.NWBAttributeSpec(name, doc, dtype, shape=None, dims=None, required=True, parent=None, value=None, default_value=None)

Bases: hdmf.spec.spec.AttributeSpec

Parameters:

• name (str) – The name of this attribute
• doc (str) – a description about what this specification represents
• dtype (str or RefSpec) – The data type of this attribute
• shape (list or tuple) – the shape of this dataset
• dims (list or tuple) – the dimensions of this dataset
• required (bool) – whether or not this attribute is required. ignored when “value” is specified
• parent (BaseStorageSpec) – the parent of this spec
• value (None) – a constant value for this attribute
• default_value (None) – a default value for this attribute

class pynwb.spec.NWBLinkSpec(doc, target_type, quantity=1, name=None)

Bases: hdmf.spec.spec.LinkSpec

Parameters:

• doc (str) – a description about what this link represents
• target_type (str) – the target type GroupSpec or DatasetSpec
• quantity (str or int) – the required number of allowed instance
• name (str) – the name of this link

neurodata_type_inc

The neurodata type of target specification

class pynwb.spec.BaseStorageOverride

Bases: object

This class is used for the purpose of overriding BaseStorageSpec classmethods, without creating diamond inheritance hierarchies.

classmethod type_key()

Get the key used to store data type on an instance

classmethod inc_key()

Get the key used to define a data_type include.

classmethod def_key()

Get the key used to define a data_type definition.

neurodata_type_inc

neurodata_type_def

classmethod build_const_args(spec_dict)

Extend base functionality to remap data_type_def and data_type_inc keys

class pynwb.spec.NWBDtypeSpec(name, doc, dtype)

Bases: hdmf.spec.spec.DtypeSpec

Parameters:

• name (str) – the name of this column
• doc (str) – a description about what this data type is
• dtype (str or list or RefSpec) – the data type of this column

class pynwb.spec.NWBDatasetSpec(doc, dtype=None, name=None, default_name=None, shape=None, dims=None, attributes=[], linkable=True, quantity=1, default_value=None, neurodata_type_def=None, neurodata_type_inc=None)

Bases: pynwb.spec.BaseStorageOverride, hdmf.spec.spec.DatasetSpec

The Spec class to use for NWB specifications

Parameters:

• doc (str) – a description about what this specification represents
• dtype (str or list or RefSpec) – The data type of this attribute. Use a list of DtypeSpecs to specify a compound data type.
• name (str) – The name of this dataset
• default_name (str) – The default name of this dataset
• shape (list or tuple) – the shape of this dataset
• dims (list or tuple) – the dimensions of this dataset
• attributes (list) – the attributes on this group
• linkable (bool) – whether or not this group can be linked
• quantity (str or int) – the required number of allowed instance
• default_value (None) – a default value for this dataset
• neurodata_type_def (str) – the NWB data type this spec defines
• neurodata_type_inc (NWBDatasetSpec or str) – the NWB data type this spec includes

class pynwb.spec.NWBGroupSpec(doc, name=None, default_name=None, groups=[], datasets=[], attributes=[], links=[], linkable=True, quantity=1, neurodata_type_def=None, neurodata_type_inc=None)

Bases: pynwb.spec.BaseStorageOverride, hdmf.spec.spec.GroupSpec

The Spec class to use for NWB specifications

Parameters:

• doc (str) – a description about what this specification represents
• name (str) – the name of this group
• default_name (str) – The default name of this group
• groups (list) – the subgroups in this group
• datasets (list) – the datasets in this group
• attributes (list) – the attributes on this group
• links (list) – the links in this group
• linkable (bool) – whether or not this group can be linked
• quantity (str or int) – the required number of allowed instance
• neurodata_type_def (str) – the NWB data type this spec defines
• neurodata_type_inc (NWBGroupSpec or str) – the NWB data type this spec includes

classmethod dataset_spec_cls()

The class to use when constructing DatasetSpec objects

Override this if extending to use a class other than DatasetSpec to build dataset specifications

get_neurodata_type(neurodata_type)

Get a specification by “data_type”

Parameters:neurodata_type (str) – the neurodata_type to retrieve

add_group(doc, name=None, default_name=None, groups=[], datasets=[], attributes=[], links=[], linkable=True, quantity=1, neurodata_type_def=None, neurodata_type_inc=None)

Add a new specification for a subgroup to this group specification

Parameters:

• doc (str) – a description about what this specification represents
• name (str) – the name of this group
• default_name (str) – The default name of this group
• groups (list) – the subgroups in this group
• datasets (list) – the datasets in this group
• attributes (list) – the attributes on this group
• links (list) – the links in this group
• linkable (bool) – whether or not this group can be linked
• quantity (str or int) – the required number of allowed instance
• neurodata_type_def (str) – the NWB data type this spec defines
• neurodata_type_inc (NWBGroupSpec or str) – the NWB data type this spec includes

add_dataset(doc, dtype=None, name=None, default_name=None, shape=None, dims=None, attributes=[], linkable=True, quantity=1, default_value=None, neurodata_type_def=None, neurodata_type_inc=None)

Add a new specification for a subgroup to this group specification

Parameters:

• doc (str) – a description about what this specification represents
• dtype (str or list or RefSpec) – The data type of this attribute. Use a list of DtypeSpecs to specify a compound data type.
• name (str) – The name of this dataset
• default_name (str) – The default name of this dataset
• shape (list or tuple) – the shape of this dataset
• dims (list or tuple) – the dimensions of this dataset
• attributes (list) – the attributes on this group
• linkable (bool) – whether or not this group can be linked
• quantity (str or int) – the required number of allowed instance
• default_value (None) – a default value for this dataset
• neurodata_type_def (str) – the NWB data type this spec defines
• neurodata_type_inc (NWBDatasetSpec or str) – the NWB data type this spec includes

class pynwb.spec.NWBNamespace(doc, name, schema, full_name=None, version=None, date=None, author=None, contact=None, catalog=None)

Bases: hdmf.spec.namespace.SpecNamespace

A Namespace class for NWB

Parameters:

• doc (str) – a description about what this namespace represents
• name (str) – the name of this namespace
• schema (list) – location of schema specification files or other Namespaces
• full_name (str) – extended full name of this namespace
• version (str or tuple or list) – Version number of the namespace
• date (datetime or str) – Date last modified or released. Formatting is %Y-%m-%d %H:%M:%S, e.g, 2017-04-25 17:14:13
• author (str or list) – Author or list of authors.
• contact (str or list) – List of emails. Ordering should be the same as for author
• catalog (SpecCatalog) – The SpecCatalog object for this SpecNamespace

classmethod types_key()

Get the key used for specifying types to include from a file or namespace

Override this method to use a different name for ‘data_types’

class pynwb.spec.NWBNamespaceBuilder(doc, name, full_name=None, version=None, author=None, contact=None)

Bases: hdmf.spec.write.NamespaceBuilder

A class for writing namespace and spec files for extensions of types in the NWB core namespace

Create a NWBNamespaceBuilder

Parameters:

• doc (str) – a description about what this namespace represents
• name (str) – the name of this namespace
• full_name (str) – extended full name of this namespace
• version (str or tuple or list) – Version number of the namespace
• author (str or list) – Author or list of authors.
• contact (str or list) – List of emails. Ordering should be the same as for author